If this had happened a year ago, Booth might have been a little more hesitant to come on this little rescue trip. But being in Kansas taught him one thing for better or worse, it was fight or die. There was an apocalypse breathing down their necks. A real biblical apocalypse and not just some crazy hobo predicting the end of the world, Booth had seen it. It was a future the angels had created sure, but just because it was a mind trick didn't mean he wanted a repeat. Everything he did since then was an attempt to stop the future that they all saw. An attempt to hold onto some kind of hope that it could change. For change to happen, Sam needed Ruby. If they were all together, somehow Booth was still confident that things would be different despite all the obstacles in their path.
Not only that, Sam was his closest friend. Ruby was important to him. As insane as it might have sounded the Agent would walk into hell for either one of them if it meant keeping everyone together. Together they were stronger, he had faith in that strength. He wasn't about to let Sam fall apart if he could help it. Shooting a man wouldn't phase him much anymore after all the lives he'd taken the last two years, but Sam was different. For half a second he looked at the younger man with a hint of concern.
That moment of distraction caused him to lose focus and have his arm grazed by a knife. He didn't respond to the hunters words, he shifted his gun to the other arm and fired at the knife holding hunter point blank. Hunters were coming out of the wood work. It worried him. He saw another just behind Sam and fired again.